I was thinking about this earlier...though I thought that Fan Protect was always on O.o I know it messed me up the first day I had that mobo
Anyway, try to connect some other fan to the CPU fan connection... See if it'll register another fan and perhaps something's just wrong with the CPU fan? Even just the RPM portion...
Hmm... I'm not sure about those 3 beeps... Typically, when it doesn't have a fan(at least from what thought I rememberd) it would just power off. You know, spin the fans for a second, then cut right back off...
Oh, something else we havn't touched on, but that's the PSU. I kind of doubt it, but they always cause weird problems and seem to be one of the first components to die out... It's worth a shot if you have another one to test...